a brief history of life sciences crowdsourcing initiatives · the goal of the challenge is to...
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308/5,000+
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Heritage Provider Network Health Prize (HPN Prize)Heritage Provider Network The goal of the challenge is to develop a breakthrough algorithm that uses available patient data to predict and prevent unnecessary hospitalizations.
1,979
ParticipationAwards Monetary Award
High Impact PublicationTravel Grant
Gift card
Reception
Name and description of initiative and organisersYear
A brief history of life sciences crowdsourcing initiatives
No Award
© 2017 sbv IMPROVER
Disclaimer:The above timeline was prepared from publicly available information – any actual or perceived inaccuracies are unintended. The timeline is provided for informational purposes only. The initiatives and organizers identified in the timeline are not, unless specifically stated otherwise on this website,
CASP http://predictioncenter.org/
KDD Cup http://sigkdd.org/kddcup/index.php
CAMDA http://dokuwiki.bioinf.jku.at/doku.php/camda
CAPRI http://www.ebi.ac.uk/msd-srv/capri/capri.html
Trec Genomics Track http://ir.ohsu.edu/genomics/
Biocreative http://biocreative.sourceforge.net/
MAQC http://www.fda.gov/ScienceResearch/BioinformaticsTools/MicroarrayQualityControlProject/default.htm
DREAM http://www.the-dream-project.org/challenges
Foldit http://fold.it/portal/ http://www.wired.com/medtech/genetics/magazine/17-05/ff_protein?currentPage=all
CAGI https://genomeinterpretation.org/
The Assemblathon http://assemblathon.org/post/44431962184/assemblathon-1-participants
CAFA http://assemblathon.org/post/44431962184/assemblathon-1-participants
Wiki project http://genes.childrenshospital.org/gene-partnership-contest/about-the-clarity-challenge/computational biology
GE Healthymagination http://healthymagination.com/
CLARITY http://genes.childrenshospital.org/gene-partnership-contest/about-the-clarity-challenge/
HPN Prize http://www.heritagehealthprize.com/c/hhp
uBiome http://www.wired.com/geekdad/2012/11/ubiome/
Crowdsourced coders take on http://blogs.nature.com/news/2013/02/crowd-sourced-coders-take-on-immunology-big-data.html immunology big data
Critical Assessment of http://www.cami-challenge.org/
Metagenomic Interpretation
Data sources:
participating in the organization and running of the sbvimprover challenges. Their inclusion in the timeline is not an endorsement by the organizers of the initiatives (including the individuals and their organizations) of the Challenge Organizers or the sbv IMRPROVER challenges.
sbv IMPROVER species translation challengePMI and IBM
Addressing the limitation in which biological events observed in rodents can be translated to humans.
122
50
Crowdsourced coders take on immunology Big DataResearchers at Harvard Medical School & Harvard Business SchoolAnalysing the genes involved in the production of antibodies and immune-system sentinels called T-cell receptors.
Crowdsourcing the Human MicrobiomeuBiome, a biotech out of the California Institute for Quantitative Biosciences (QB3) uBiome is crowdsourcing the sequencing and mapping of the human microbiome.
514
GE’s HealthymaginationGE, Kleiner Perkins Caufield & Beyers, Mohr Davidow Ventures, Venrock, and MPM CapitalAn open call to action for oncology researchers, businesses, students, and healthcare innovators to submit ideas that will accelerate innovation in breast cancer.
54sbv IMPROVER diagnostic signature challengePMI and IBM
Test and develop different approaches to classifying clinical samples based on gene expression.
23
215
Children’s Leadership Award for the Reliable Interpretation and appropriate Transmission of Your genomic information (CLARITY)Boston Children’s Hospital
To identify best methods and practices for the analysis, interpretation and reporting of individuals’ DNA sequence data, to provide the most meaningful results to clinicians, patients and families.
CAMI is an initiative to evaluate methods in metagenomics.
2010
sbv IMPROVER network verification challengePMI, Selventa and IBMTo engage the scientific community to review, challenge as well as make corrections to the conventional wisdom on molecular mechanism of the respiratory system. Second network verification challenge ran until 2015.
sbv IMPROVER systox computational challengePMI
Alice McHardy, HZI Braunschweig; Thomas Rattei, University of Vienna; Alexander Sczyrba, Bielefeld University
Designed to verify that a robust predictive signature can be extracted from gene expression data that differentiates smokers, former smokers, and never smoker subjects.
sbv IMPROVER Singapore datathonPMIDesigned to analyze big data in the field of epigenomics and extract biological knowledge.
sbv IMPROVER Israel epigenomics challengePMIDesigned to predict class labels of different exposed groups based on epigenomics and transcriptomics data.
sbv IMPROVER Japan biological interpretation datathonPMIDesigned to assess biological interpretation and quantification of biological impact based on omics datasets.
Critical Assessment of Metagenomic Interpretation
73
WikiProject Computational Biology
Wikipedia
Aimed at improving and organising articles on Computational Biology, Bioinformatics, Computational Systems Biology and related topics.
2010
50
WikiProject Computational Biology
Wikipedia
Aimed at improving and organising articles on Computational Biology, Bioinformatics, Computational Systems Biology and related topics.
Critical Assessment of protein Function Annotation algorithms (CAFA)The Automated Function Prediction Special Interest Group
Experiment designed to provide large-scale assessment of computational methods dedicated to predicting protein function.
19
The AssemblathonUC Davis Genome Center
Offshoots of the Genome 10K project, these contests assess state-of-the-art methods in the field of genome assembly.
The Critical Assessment of Genome Interpretation (CAGI)Steven Brenner, computational genomicist, University of California& John Moult, computational biologist, University of MarylandAn experiment to objectively assess computational methods for predicting the impacts of genomic variation.
2010-
2013
240,000
FolditDavid Baker, biochemistry professor University of Washington Seth Cooper, lead designer Foldit is an online puzzle video game about protein folding to help scientists solve “real world” problems.
135
Submissionsper challenge
80
Dialogue for Reverse Engineering Assessments and Methods - DREAMGustavo Stolovitzky, IBM Computational Biology Center The main objective of DREAM is to catalyze the interaction between theory and experiment, specifically in the area of cellular network inference and quantitative model building.
36
MicroArray Quality Control (MAQC): MAQC-IIFDA micro-array platform providers, RNA suppliers, EPA, NIST, academic laboratories and other stakeholdersAssess the capabilities and limitations of various data analysis methods in developing and validating micro-array based predictive models.
137
MicroArray Quality Control (MAQC): MAQC-I FDA micro-array platform providers, RNA suppliers, EPA, NIST, academic laboratories and other stakeholders
Provides quality control (QC) tools to the micro-array community to avoid procedural failures.
23
Critical Assessment of Information Extraction systems in Biology (BioCreAtIvE)Personnel from CNIO, MITRE, NCBI, IntAct/MINT and EBI
BioCreAtIvE compares methods and the community assessment of scientific progress.
2004&
2006Submissionsper challenge
Participants
Teams
34
TREC Genomics Track William Hersh, National Science Foundation IT Programme
A workshop for evaluating systems for information retrieval and related technologies in the genomics domain.
2003-
2007Submissionsper challenge
36
Critical Assessment of PRediction of Interactions (CAPRI)A management team formed of EMBL/EBI-PDBe Group
A blind prediction experiment whereby participant predictor groups are given the atomic coordinates of two proteins that make biologically relevant interactions.
20
Critical Assessment of Massive Data Analysis (CAMDA) Simon Lin and Kimberly Johnson from the Duke University Bioinformatics Shared Resource
Founded to provide a forum to critically assess different techniques used in micro-array data mining. Submissions
per conference
122
Knowledge Discovery and Data mining Cup (KDD Cup) Association for Computing Machinery's Special Interest Group (ACMSIG)
The annual competition for Knowledge Discovery and Data Mining.
1997-
2010
Average numberof teams perexperiment
Average numberof participants
per competition
Average numberof submissions
per round
169
Critical Assessment of Protein Structure Prediction - CASP*John Moult, University of Maryland Biotechnology InstituteCASP is a community-wide, worldwide experiment for protein structure prediction taking place every two years.
Recurrent
or one-off
Average numberof submissionsper experiment
Average numberof participants
per year
Average numberof participants
per contest
Participants
Participants
Participants
Participants
Participants
Participants
Participants
Teams
Teams
Ideas
Average numberof participantsper challenge
Nb of participants/contributions
Nb of participants/symposium attendants
$
$
$
$
$100,000
$3,230,000
$60,000
$6,000
$25,000
$50,000
$50,000
$15,000